pVAC-Seq is written for Linux but some users have been able to run it successfully on Mac OS X. If you are using Windows you will need to set up a Linux environment, for example by setting up a virtual machine.

pVAC-Seq requires Python 3.5. Before running any installation steps check the Python version installed on your system:

python -V

If you don’t have Python 3.5 installed, we recommend using Conda to emulate a Python 3.5. environment. We’ve encountered problems with users that already have Python 2.x installed when they also try to install Python 3.5. The defaults will not be set correctly in that case. If you already have Python 2.x installed we strongly recommmend using Conda instead of installing Python 3.5 locally.

Once you have set up your Python 3.5 environment correctly you can use pip to install pVAC-Seq. Make sure you have pip installed. pip is generally included in python distributions, but may need to be upgraded before use. See the instructions for installing or upgrading pip.

After you have pip installed, type the following command on your Terminal (for Mac and Linux users) or the Command Prompt (for Windows users):

pip install pvacseq

You can check that pvacseq has been installed under the default environment by listing all installed packages:

pip list

pip will fetch and install pVAC-Seq and its dependencies for you. After installing, you can run pvacseq directly from the Terminal/Command Prompt.

If you have an old version of pVAC-Seq installed you might want to consider upgrading to the latest version:

pip install pvacseq --upgrade

Getting Started

pVAC-Seq provides a set of example data to show the expected input and output files. You can download the data set by running the pvacseq download_example_data command.

The example data output can be reproduced by running the following command:

pvacseq run \
<example_data_dir>/input.vcf \
Test \
HLA-G*01:09,HLA-E*01:01,H2-IAb \
NetMHC PickPocket NNalign <output_dir> \
-e 9,10 \
-i <example_data_dir>/additional_input_file_list.yaml --tdna-vaf 20 \
--net-chop-method cterm --netmhc-stab \
--top-score-metric=lowest -d full --keep-tmp-files

A detailed description of all command options can be found on the Usage page.